Heir of ROOT
by DeathByShyKid
Summary: One some spur of the moment, Naruto finds himself helping a shinobi of darkness. Through this one encounter of life-saving events, Naruto and this man grow closer through a family-type of a bond. Awaiting the two are great adventures and many challenges. Father-like Danzo, sort of good Danzo, family-like ROOT(but not really), strong Naruto, smart Naruto, mature Naruto, slow updates
1. Chapter 1

**Disclaimer: I do not own Naruto or any characters that belong to it. I only own the idea and plot.**

 **Summary: One some spur of the moment thought, Naruto finds himself helping a shinobi of darkness. Through this one encounter of life-saving events, Naruto and this man grow closer through a family-type of a bond. Awaiting the two are great adventures and many challenges.**

* * *

Danzō sighed slightly, staring down into his teacup. The warm tea fragrance filled his nostrils, gazing into the pools of gold deliciousness. He rarely got to enjoy his times like this in the confinement of a home he hadn't been in for months. It was pleasant. Well, mostly. His mind was warped with thoughts that plagued him. Most were of worries of an unforsaken future and the rest was of undetermined consequences of actions that need to be taken soon. It wasn't that he as a person was scared, but rather fearfully for his village that he's taken so much pride upon. However, one thought stuck out the most.

Konohagakure needs to be protected.

But how? How could he do what he's sworn to do since he was a child in the academy? How does he protect an entire village if it's just falling apart from the inside? How can he help his village?

In reality, there is a hell of a lot of things that Danzō could do that would greatly benefit Konohagakure. He had money, so much that he could practically build his own smaller village. He had connections all over the world, so exporting could be increased exponentially. He had the knowledge that comes with old age, enough so that he could teach almost all the newer generations. He was wise when it comes to his strengths, so he could lead a whole army to victory. Though, that doesn't mean that Danzō should go forth with any of these.

It was better to stay quiet and in the background. After all, a ninja's best quality is their use of deception.

He took another sip of his tea, letting the warmth coat his throat. Yes, such a way of living was fit for someone like him. He ran everything from the shadows; nothing went by him without him noticing. His version of the Third Hokage's ANBU, ROOT, was for doing things from the darkness. They found out more information that the ANBU and were more controlled than the Hokage's agents. They were quick on their feet and knew how to get the job done. The ROOT worked well together and independently; a little _too_ well. They were loyal to him and him alone. They didn't report back to anyone except Danzō.

They were great soldiers.

A sudden shuffling entered his ears. He made sure not to stiffen in surprise; better let the intruder think that they were still hidden. One thing is true about Danzō, nothing ever goes past him. Nothing. Not even this intruder who has managed to pass the force field surrounding his compound and entered his home.

He stood up, an empty tea set in his arms as he headed towards the kitchen. While he lived in a large compound, he lived alone. Danzō didn't trust enough people to let some maids or servants walk around his home.

Dropping off the dishes in the sink, he turned around and walked towards the extended hallway in his compound. The shuffling continued from somewhere around him. He concentrated on finding where the intruder was based on the noises he was hearing. Danzō internally smirked, using his good arm to punch through the ceiling in the hallway. The audible shriek filled the room as a blond-haired child fell to the ground. Danzō's eyebrows furrowed together before realizing who the child was.

The Kyuubi Jinchuriki, Naruto Uzumaki.

" _Well, this is unexpected."_ He thought to himself as the child no older than six picked himself up from the ground. Danzō gave the kid a quizzical look, "What are you doing in my compound, boy?"

Naruto looked up with wide eyes as words started to form in his throat, "I-I-I-"

"You are wasting my precious relaxation time." He replied, already finding himself annoyed by the six-year-old, "Speak or leave immediately."

"W-Wait!" His chest rose and deflated in quick succession, "I, uh… um… I wanted t-to warn you… about s-someone."

Danzō was not expecting this, "Really now? Who would that be?"

A determined look suddenly filled Naruto's eyes but decided to whisper instead of burst out in shouts, "A bunch of the ANBU members that chase me in the village. They are planning on hurting you tonight!"

"ANBU?" He rose an eyebrow, "Are you sure?"

"Y-Yeah." He nodded slowly, "There's five of them. Two of them watch over me during the day and the other three beat me up at night. I, uh, I know what their masks look like…"

"Alright." Danzō looked around the house, "Come with me." Naruto latched onto his black cloak, glancing around the compound with fearful eyes. He stared at the blond-haired boy, "Tell me, what possessed you to sneak into my compound and inform me about this? Aren't I a stranger?"

"Um… no, not really. Hokage-Jiji talks a-about you all the time. You w-were… are… um, friends?" Naruto tried, furrowing his brows, "But, uh, I knew that Hokage-Jiji would b-be sad if those ANBU g-guys got to you."

"So you snuck in to warn me?" He supplied.

"Yeah…" Naruto looked up, "A-Am I… Am I in trouble?"

Danzō stared down at him, "If you are lying to me just to assassin me, I'd have to kill you. If you are telling the truth, I will reward you."

He gulped but shook his head, "I'm not lying, I promise."

"Promises can be broken, child, don't be so gullible." He stated.

"Oh…"

"Do you know my name?" Danzō asked, suddenly curious.

The boy furrowed his brows in thought, "Danni? Danino? Daoni? Wait, there's not I in your name, is there?" He shook his head, slightly amused. "Uh... Daz? Something with a Z in it, right?" The older man nodded, "Da… uh… Dazo? Wait, I'm getting close, aren't I?!" Excitement filled the boy's voice. The ROOT leader nodded. "Yes!" Naruto cheered, "Um… Dazno? No, wait, I've got it! Danzō!"

"Yes, my name is Danzō Shimura." He smiled slightly, "And what's your name?" He already knew the answer but decided to amuse the boy anyway.

"I'm Naruto Uzumaki!" He exclaimed, smiling brightly, "I'm going to be the next Hokage!"

"Good luck, kid," Danzō said as the two entered a lobby-type room. He looked down at the blond-haired child. Naruto let go of his cloak, leaving the man's side to look around the nicely decorated room.

"Wow~" He awed.

"Naruto." He said, catching the kid's attention, "How did you get into this compound? There is a large force field covering this whole place that can only be opened by my blood."

The Jinchuriki looked up at him, "Oh that's easy. There was a hole in the force field. It was kind of big too. I could crawl through and still have room to spare."

"So, that means that the ANBU agents that are coming to kill me could have gotten in also." He mumbled.

A look of horror filled Naruto's face as he covered his mouth, "D-Did I lead t-them in?! Oh K-Kami, I'm s-sorry. I-I didn't mean t-to, I j-just wanted to h-help."

He chuckled, "I don't think you led them in here. I believe that they already knew about it. I haven't been able to relax in my home for months. They would have had that amount of time to find weak points in the force field."

"R-Really?" He asked quietly.

"Yes, now, we need to be ready for anything." Danzō said calmly, "What were the five ANBU's masks?"

"Uh… boar, lemur, bat, tiger, and leopard. Tiger and Leopard always team up, so watch out for them." Naruto stated.

"Alright, go find a hiding spot in this room. This room masks chakra. I'll deal with the traitorous ANBU." Danzō stated.

Naruto looked around the room, hugging himself slightly, "B-But won't you get hurt? The ANBU are pretty scary."

"I'll be fine." He rolled his eyes, "Now, hurry up, I can feel their chakra in the house." The boy nodded, climbing up a bookshelf and hiding behind a few books on the top shelf. Danzō thought it to be impressive. Had he not watched Naruto climbed and hide there, you wouldn't have suspected anything. Maybe there was more to the boy than a demon sealed in his stomach.

Danzō left the room in search of the ANBU that were after him. It was at this moment that he wished to have some of his ROOT operatives patrolling his compound. Though, it couldn't be helped now. Even if he was old, he could still take down a numerous number of opponents. Especially the ANBU forces. He strolled down the hallway, eyes peeking around discreetly, feeling the faint movements in chakra somewhere in the compound. His shoulders were relaxed as if he didn't know that he was being hunted in his own home. A crackling noise came from behind him. He grinned, _"So, it begins."_

Fainting left, Danzō managed to outmaneuver the lightning that came for him. Tiger stood behind him, arms out in front of him in a taijutsu stance. Leopard appeared in front of the old man, her body hunched low to the ground, hands hovering over the wood. Almost simultaneously, Tiger and Leopard shouted out twin attacks. Water pooled around Danzō's ankles as lightning came to meet it in some sort of dance. The old man effortlessly jumped out of the way, hopping onto the wall and using chakra to stick to it. Just as quickly as he landed, he jumped away and shunshinned behind Leopard as hands came out of the wall. Boar left the wall, standing beside Tiger and Leopard. Danzō stared them down, realizing that there were still two more.

A smoke screen filled the hallway, making visibility hard. Danzō didn't need his eyes to fight in these conditions, having been in thousands of situations like these. These ANBU's were like children trying to play ninja. It was quite amusing, to say the least. Dodge a fire infused fist from Lemur and jumping up from the grappling hands of Boar, Danzō found that the was enjoying himself. A wind-powered jutsu came from behind, hitting his back and cutting him up. Bat dropped down from the ceiling, staring at Danzō. He fell to the ground, only to turn into mud. The five ANBU members looked around the area, slowly backing into each other.

The ground in between the circle of ANBU appeared Danzō, throwing both his legs out, effortlessly kicking Boar and Tiger in the chest. He did a one-hand cartwheel towards the right, getting some distance between himself and the ANBU. Lemur flanked left, hand coming to mouth, uttering a jutsu. A large fireball filled the hallway, catching the hallways on fire in its wake. Danzō shunshinned to a different part of the house. He then realized that he was inside of the lobby and that the ANBU were quickly approaching.

"Are you okay?" Naruto whispered from the top shelf, poking his head out from the books.

"Yeah, I'm fine. Keep hiding. I'll come back for you." He stated, doing another shunshin. He disappeared.

Naruto looked at the spot where the older man had once been. He frowned in worry. _"I really hope that he'll be okay."_ He thought to himself, _"What happens if he gets hurt? Hokage-Jiji will get sad and so will Konoha. What do I do?"_ The six-year-old stared at the door. _"But he told me to keep hiding."_ He reasoned with himself, _"He'll come back for me…"_ The more that Naruto stared at the wooden door, the more that the thoughts kept coming back. _"But… if he doesn't come back for me, that means that he's d-died, right?"_ He questioned, _"Oh Kami… what do I do?"_ Naruto sighed, realizing that there is only _one_ thing to do in these situations. Kicking the books away, revealing his spot, Naruto climbed down the large bookshelf. He rushed towards the door, opening it slightly. He peeked out and noticed that there wasn't anyone in the hallway. Nodding to himself, Naruto slipped out of the lobby-like room and into the hallway.

The fire had overtaken the west parts of the compound due to Tiger and Lemur teaming up to set things on fire. Along with Bat enhancing the ferocity of the flames, well, let's just say that it was getting annoying for Danzō as he fought off the five ANBU by himself. He's going to tear Hiruzen a new one for having such traitorous ANBU members. Leopard started shooting water bullets as Bat started to fight with taijutsu up close. It was like child's play watching Bat try and hit him with his fists. Though, it was kind of distracting dodging punches, kicks, water bullets, great fireballs, and constantly trying to not get sucked underground by Boar. He wasn't being pushed back by the five ANBU, he was simply trying to get more distance between them and himself. Though, luck didn't seem to be on his side now because just when he thought he was getting a little farther from them, one of them would appear and put him back on the defense.

" _I fucking hate ANBU."_ He grumbled to himself, punching the shit out of Leopard. The sudden sound of metal hitting a body before falling to the ground filled the hallway. All movements stopped as Danzō glanced behind him, seeing Naruto holding a metal bat that was partially colored red. Beside him was another ANBU member with a hummingbird mask on, blood trickling out the back of his head. Fear and shock were present in the boy's eyes.

He didn't even notice him.

He glanced up at the older people, "H-He was trying t-to hurt you…" Danzō nodded, hopping towards the boy and swiftly picking him up. Naruto couldn't seem to let the metal bat go, his hands grasped so hard around it that his knuckles were turning white.

"Good job." Danzō praised. The boy didn't say anything back. He stared at the man as the founder of ROOT rushed away from the ANBU with fast steps.

"They are going to try and trap you in the hallway again," Naruto mumbled, still shocked that he had killed a man.

"Got it." He stated, taking a left turn into a room. He shut the door behind him. Danzō rushed over to a desk, opening the bottom cabinet. There was a silver button in the back. Quickly pressing it, the older man ran over to the door that had appeared from the wall.

"Where are we going?" Naruto asked.

"There are secret passages all over this place," Danzō informed, the door closing behind him. He took out a brick from the wall inside the secret passage, pressing a red button. A ticking noise filled the air. Danzō picked up his pace, using a few shunshin to get farther inside the secret passageways. The ticking was becoming quicker and more prominent. Naruto was getting worried. It was only when the two managed to get to the surface above the Hokage Monument did the ticking noise become so quick that it was almost inaudible. A booming noise filled the area as Naruto's eyes widened. Danzō had blown up his compound and those ANBU inside. The older man looked down at the shocked boy, "Come on, we've got to inform the Hokage." Naruto nodded numbly as they took off towards the Hokage's office in the middle of the village.


	2. Chapter 2

**Disclaimer: I do not own Naruto or any characters that belong to it. I only own the idea and plot.**

 **Summary: One some spur of the moment thought, Naruto finds himself helping a shinobi of darkness. Through this one encounter of life-saving events, Naruto and this man grow closer through a family-type of a bond. Awaiting the two are great adventures and many challenges.**

* * *

 **Previously on Heir of ROOT**

 _"Where are we going?" Naruto asked._

 _"There are secret passages all over this place," Danzō informed, the door closing behind him. He took out a brick from the wall inside the secret passage, pressing a red button. A ticking noise filled the air. Danzō picked up his pace, using a few shunshin to get farther inside the secret passageways. The ticking was becoming quicker and more prominent. Naruto was getting worried. It was only when the two managed to get to the surface above the Hokage Monument did the ticking noise become so quick that it was almost inaudible. A booming noise filled the area as Naruto's eyes widened. Danzō had blown up his compound and those ANBU inside. The older man looked down at the shocked boy, "Come on, we've got to inform the Hokage." Naruto nodded numbly as they took off towards the Hokage's office in the middle of the village._

* * *

Once Danzō had entered the building that his long-time friend worked in, he placed the boy who had been in his arms on the ground. Naruto reached out and grabbed the bottom of the older man's cloak frantically, having never liked the Hokage's office for people always stared at him. Now at ground level, the child started to notice many things now that his face wasn't buried in Danzō's chest. Like how the receptionist liked to smoke inside the building while staring blankly into space. Or how an elderly couple kept glaring at him whilst standing in the corner talking amongst themselves. Or that many of the ninja inside bowed to Danzō and made room for him. Like how his heart pounded in his chest.

The two of them started to climb the steps of the building that held the Third Hokage. People were bustling about in quick succession. Civilians inside the building looked frantic, panic crossing their features. The ninja tried to get answers out of Danzō but he just kept walking on. Sometimes Naruto would catch the older man looking down at him as if Danzō was making sure that the boy was still there. It made him feel happy to think that the older man was doing such a thing.

It was only a few minutes later did the two find themselves standing in front of the Hokage's office door. People were conversing in great detail, their voices trailing into the hallway where Danzō and Naruto could hear partial amounts from the conversation. The older shinobi didn't bother knocking on the door like some diplomat. Instead, he opened the door and waltzed in with such an aura of authority. All the while, Naruto was still holding onto Danzō for dear life.

The many amounts of people inside the room ceased all conversation with wide eyes.

At their entrance, Hiruzen instantly stood up. He looked Danzō up and down before giving a sigh of relief, seeing no visible marks on his old friend's body, "I'm glad that you are alright, Danzō."

"I probably wouldn't have had Naruto not shown up in my home this evening," Danzō replied smoothly.

At that moment, it seemed that everyone finally noticed the blond-haired boy attached to Danzō's leg. "Naruto?" The Hokage blinked in surprise, looking between his successor's son and his old friend. His eyebrows furrowed together in question, utter disbelief written on his face, "I'm not sure that I understand."

"I, um…" An embarrassed blush filled Naruto's cheeks as all eyes settled on his small frame. The words felt constricted in his throat.

"He was the one to inform me that several members of the ANBU were planning on my assassination tonight." Danzō supplied, "Had he not crawled through the hole in the force field of my compound and snuck inside the house, I could have been killed."

"Naruto," Hiruzen started, his dark eyes piercing to the six-year-old, "…you were there?"

"Y-Yeah."

"How did you know?" An abrupt ANBU member spoke up from the crowd.

"U-Uh… Um…" Too many people were staring at him. The looks on their faces could tell that there was some sort of resentment towards him. It made him nervous. His hands tightened on Danzō's cloak. He glanced up at the older man, hoping that Danzō could supply the words for him again. Instead of an annoyed or angry face staring back at him, it was soft and kind-looking. _"You can do this."_ Either Danzō was sending him a mental message or Naruto was hyping himself up. He guessed it to be the second one.

 _"Well…_ " The same ANBU member from before was letting his aggravation show.

Naruto took a deep breath, visibly trying to relax himself. "So, there are two of these ANBU that… um… Hokage-Jiji made them watch over me during the day. Well, I overheard them talking a few days ago about a compound on the edge of the village. A friend of Hokage-Jiji's lived there and they said that they were going to kill him." Naruto suddenly looked uncomfortable speaking to so many people, "I decided to… do something bad."

"What did you do, Naruto?" Hiruzen asked the boy.

"I may have stalked them for a few days to try and figure out what was going on, who they were targeting, who was involved, and where the target was living." He looked away in embarrassment.

"Why didn't you inform me?" The Hokage asked.

The blond-haired boy stared at him, "I was in too deep. If they knew that I knew as much as I did, they'd… probably kill me. I can outrun almost all the ANBU – most of the time – but I can't fight them. Plus, there were _five_ of these guys. It's selfish, but if I had told, I would have been killed."

"But how did you get into Danzō-sama's compound? It is impossible to get in with his blood." Someone voiced.

"That was easy." Naruto started with a little excitement in his voice, not noticing the shocked faces of those around him, "There was a pretty big hole in the force field that I could crawl through."

The Hokage looked up at Danzō, "I'm guessing that those rouge ANBU members had probably already known about this."

"You'd be correct. I hadn't been in my compound for months. Those ANBU were just waiting until I appeared at my compound to strike." Danzō stated.

"Let me get this straight. Naruto overhears the ANBU members I sent to look after him – which is a feat in and of itself – that they were going to kill a friend of the Hokage's and proceeded to stalk these members. He finds out who all is involved, where the attack was going to take place, and who the target was. He then decides to go over to Danzō's compound to warn him that he was being targeted. Then, Danzō fights the ANBU members." Hiruzen's face suddenly became thoughtful, "If I've gotten correct, I still have one more question."

"What is it?" His long-time friend questioned.

"How the hell did your compound end up exploding?" The Third Hokage asked, "Danzō, you should have been able to take out those ANBU members with no problem but your compound _explodes_?! I think you can see why I'm confused."

"I really couldn't go all out while Naruto was in the compound. I would have probably hurt or killed him on accident had I gone all out. So, I was at a slight disadvantage. They had also set my compound on fire and it was spreading. I was fighting against falling debris and trying to not catch on fire while also fighting against five different ANBU members who were extremely good at coordinating with each other." Danzō explained, looking annoyed, "There was a sixth ANBU member that Naruto didn't notice and had kept hidden for a good majority of the night. He came up behind me and had Naruto not swatted him over the head with a metal bat, I'd probably be in the hospital or dead. By this time, most of the compound was on fire so I decided that resulted in the compound exploding. I have a secret passage in my compound in case something happened. Inside is a button that will make my compound self-destruct. There, now you know why my compound exploded."

The Hokage nodded slowly, looking at Naruto, "Which of the ANBU members were involved?"

"Tiger and Leopard are the ones that you assigned to me. Boar, Lemur, and Bat were the other three that I knew about. Hummingbird was the sixth one that came out of nowhere." Naruto stated.

You could physically see almost all the ANBU in the room tense up at the mention of their members' name. Hiruzen nodded, "Thank you for your time. Danzō, Naruto… I'm glad you both are okay. I was worried when there were reports flooding in about an explosion. I thought we were being attack."

"You're welcome," Danzō stated.

"You're dismissed for now. If there is anything else, I will call for you." The Third Hokage said, waving them off with a smile. Danzō turned quickly, the cloak slipping for Naruto gripping hands. The older man waltzed out of the room with fast steps. The blond-haired boy spun on his heel, running out of the room. His tiny legs wouldn't let him go as fast as he wanted.

"W-Wait!" He called out, seeing Danzō walk out of the building. He ran as fast as he could, slamming the door open, seeing the older man start to take steps away from the Hokage's office. "Wait! Please!" He shouted out.

Danzō stopped, turning his head to look at the boy, "What do you want?"

He ran up to him, "I need to say something."

"What is it?" He questioned.

"I know that I didn't do much when you were attacked and I feel awful because of it. All I did was stalk someone and get in your way. You said it yourself, since I was there, you weren't able to fight to the best of your abilities. I'm also a coward… I was so scared to leave that room. I just…" Naruto stared the older man in the eyes, "You're strong, really strong. I saw just how strong you were near the end of the fight when I… _killed_ that guy. I want to be that strong. I guess what I'm trying to ask is… will you train me?"

Danzō's eyes widened. For years, ever since the day of Naruto's birth, he's begged Hiruzen to give the boy to him to train. He had never expected that such an opportunity would present itself to him. These cards that had never been dealt with him were already in his pocket. He tried to hide his grin that wanted to appear on his face, "Are you sure?"

"Yes!" Naruto nearly shouted out, hands close to his chest while being balled into fists.

"I'm not so sure. I'm the leader of an underground unit called ROOT. We're like ANBU but better and more _secretive_. Training is hell. I'm not sure that you'd last." Danzō said, "You said yes too quickly. You've barely thought this through. By wanting me to train you, you are signing yourself up for a lifetime job. Becoming Hokage would no longer be in your sights. Your whole life, personality, wisdom, outlook… everything, it's all going to change. Are you _sure_ that you want to be trained in the way of ROOT?"

Naruto took a deep breath, seriousness falling over his face, "Yes."

Danzō let the grin spread on his face, "Fine, then. Meet me here tomorrow at five in the morning. Bring nothing. I hope you know what you're doing, Naruto, because your life is about to change." With the words said, Danzō disappeared with a swirl of leaves.

Naruto stared at the leaves and smiled, _"I know what I'm doing."_

* * *

 **A/N – I'm terribly sorry everyone. School's a bitch. Luckily, it's ending in two weeks. In two weeks, I'll be writing like crazy. I'll probably be posting chapters left and right for anything and everything. I only got around to writing this chapter because I had a bout of writing inspiration so I ditched this review that's due in a few days to write this. Praise me for the chapter I slaved over instead of doing schoolwork. I hope that you like and I will try to get more chapters out for all my fanfictions… hopefully.**


	3. Chapter 3

**Disclaimer: I do not own Naruto or any characters that belong to it. I only own the idea and plot.**

 **Summary: One some spur of the moment thought, Naruto finds himself helping a shinobi of darkness. Through this one encounter of life-saving events, Naruto and this man grow closer through a family-type of a bond. Awaiting the two are great adventures and many challenges.**

 **Previously on Heir of ROOT**

"… _Are you_ sure _that you want to be trained in the way of ROOT?"_

 _Naruto took a deep breath, seriousness falling over his face, "Yes."_

 _Danzō let the grin spread on his face, "Fine, then. Meet me here tomorrow at five in the morning. Bring nothing. I hope you know what you're doing, Naruto, because your life is about to change." With the words said, Danzō disappeared with a swirl of leaves._

 _Naruto stared at the leaves and smiled, "_ I know what I'm doing _."_

Naruto stood there, staring like a moron at where Danzō had been before he disappeared. Tears started to rise in his eyes, bubbling up. He turned away, walking towards his apartment. His heart thumped wildly in his chest, the hammering continuing its way towards his ears. Naruto found that he couldn't hear much except the constant pounding ringing in his ears. The tears still lingered even as he entered his home. They didn't start falling until he had flopped onto his bed and stared up at the ceiling. Hands clamped over both of his eyes to stop the waterworks.

"W-What am I _thinking_?!" He exclaimed to no one, "I j-just met this guy! I don't k-know _who_ he is, what he's going to _do_ , a-and… why was I so _sure_ that I'd be able to handle it… Do I _really_ know what I'm doing? Maybe I should have thought this through…" Naruto wiped away the tears, going back to staring at the ceiling. He sighed, "No… I know what I'm doing… I think… wait…" He gave a huff, curling on his side and closing his eyes. The blond-haired boy stared at his hands, "I can never be Hokage… That was the _only_ way that anyone would ever acknowledge me… Am I _sure_ that I want to do this? Do I really want to give up my dream to train under Danzō?" Naruto sighed, sitting up, not feeling tired right now.

Standing up, he walked towards the kitchen for a glass of water. He pulled out a glass, "I already said I would do it… It'd make Danzō feel bad if I were to just _bail_ out of nowhere… but, I wonder if he'd understand if I told him that I… No…" He turned on the faucet. Placing his glass under the faucet, Naruto watched the water fill up the glass. "I never go back on my word… I technically gave him my word, so… that means that I can't go back." He took a sip, staring at the sink with lost eyes, "What do I do? Do I stay who I am and become Hokage by any means… or do I… do I go tomorrow to meet up with Danzō and get training? If I go with the first option, I would have to wait even _longer_ to get trained by anyone. I'd have to wait till I graduated from the Academy in a few years to even get _close_ to getting some advanced level of training." He took another guzzle of water, emptying the rest back into the sink. Naruto ran a hand through his hair as he went back to his bed, the moonlight shining through his window. "However, if I go with the second option… I wouldn't be able to be Hokage… I wouldn't be able to achieve my goal… but, I would get trained faster and better. I may not be able to be Hokage but that doesn't mean that I won't be acknowledged by the village." He tapped his chin, "Maybe Danzō can help me with that? He seems pretty nice…"

He let out a nice, long yawn, blinking his eyes tiredly. Naruto pulled off his pants and t-shirt, climbing under the covers with only his boxers on. A blissful dream of acknowledgments filled his mind as he slumbered.

Danzō gave a grin, watching the six-year-old boy climb in bed after ranting to himself for almost twenty minutes. He didn't mean to be so curious about someone, it's just that this was a _someone_ that would be joining his ROOT organization. He shunshinned from the boy's apartment, appearing inside of one of the ROOT's many meeting rooms. Oh, he can't wait to see Hiruzen's face when he tells him that Naruto _wanted_ to work with him – to be trained by _him_. Not the academy. Him.

It would be a sight to see.

 **A/N – I know it's short, but I just couldn't think of what else to put in here. Next chapter will be better, I promise. As Naruto taught me, you never go back on your word and I will live by that so long as I keep writing fanfictions.**


	4. Chapter 4

**A/N – Hello once more! I am back, writing for some of my older fanfictions since I'm on my break from 'He's My Son' and 'The Great Medic'. And guess who's back for another chapter? 'Heir of ROOT'! Woo! Well, it's a little less than 2000 words which is sad but the chapters will slowly start to get longer and longer as the story progresses. Just to let you know:**

 **1\. I'm getting rid of the summary for the remaining chapters of this story because I'm sure you all get the point by now. The disclaimer will still remain though because I'm lazy and I don't want to get into legal trouble, you know?**

 **2\. Major time skip in the next chapter. I am going to be skipping all the tiny things from Naruto's ROOT training but that is because I'm saving flashbacks of the training for later on in the story.**

 **3\. Naruto's and Danzō's relationship will be more of a father-son type of relationship after this time skip but don't worry, many flashbacks of how they got to that point. I'm not going to be one of those lazy authors that don't write training sequences and then, boom, Naruto is over-powered for no reason.**

 **4\. Naruto will NEVER be over-powered. Someone is probably always going to be stronger than him.**

 **5\. I will be introducing random characters that I created for this story like other ROOT members that Naruto kind of got close to. Don't kill me for this.**

 **6\. NO PAIRINGS! Naruto is going to end up being asexual or something like that.**

 **Well, that's about it. Continue on with the story!**

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 **Disclaimer: I do not own Naruto or any characters that belong to it. I only own the idea and plot.**

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Naruto wrung his hands together in an anxious stupor, walking down the quiet streets. Some shops had already started opening their shops; I guess the saying 'early bird gets the worm' would be appropriate for the shop owners who were already selling their products to the early morning people. His eyes shifted nervously around the streets, gazing into a shop for the time. _"Calm down, Naruto."_ He cooed mentally to himself, _"You have twenty minutes until you have to be there, slow down."_ Still, despite his mental serenity, his heart was still pumping erratically while his eyes stared into shops once more for a triple check on the time; seventeen minutes until he was supposed to meet Danzō outside of the Hokage's office.

Naruto was almost there, the Hokage's office just in his sights. The very thought made his breathing accelerate and heart rate sped up. He felt jumpy, a bubbling and churning sensation in his stomach, last night's thoughts still plaguing him even hours after the fact. Sure, he knew he wanted to get stronger and that he was ambitious but, was this _really_ what he wanted? Did he want to spend the rest of his life in the shadows of the world to do the village's dirty work? The blond-haired boy sighed quietly, arriving at the spot where he would meet Danzō. He looked across the street for the time – the sixth time this morning – only to find that he had eight minutes until the designated time. Maybe Danzō would be early or would he show up later than the chosen time? What if he didn't show up at all?

"You need to stop worrying." A deep, serious voice stated from behind him. Naruto jumped slightly, squeaking in surprise as he twisted around, seeing the scarred face of Danzō.

He looked down, "Sorry, I'm just… conflicted?"

"I thought you were sure?" He raised an eyebrow.

"I was… until I was left alone with my thoughts and I kept doubting myself." Naruto admitted, "I'm leaving the very dream I've been striving for since I could have coherent thoughts."

"Then, what do you choose? You have one last chance to prove that you are sure that you want to join the ROOT organization." Danzō stated with the utmost seriousness on his face.

The younger of the two fell silent for a few seconds before making eye contact with the man, "I feel more positive than I did yesterday. My dream has always been to be acknowledged by the village and I thought that I could only do that if I were to become Hokage… but, maybe there is another way? Maybe I don't have to go all out to prove myself like becoming Hokage. I could be acknowledged by ROOT, right?"

He nodded, "You would be acknowledged not only by the village but by the entire world."

The blond-haired boy smiled slightly, "So… yes, I'm not completely sure that I would want to join ROOT."

"Fantastic." The older man said, "Come with me, I will show you where you will stay and then we will officially start your training."

"Thank you, Danzō-sama." Naruto smiled appreciatively.

"No need to thank me yet." Danzō grinned.

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Hiruzen smoked his pipe, checking the time on his watch. He had about ten minutes until a monthly meeting was commenced. He was taking this time to smoke a little bit before anyone stopped him and keep to his thoughts. Strange things have started to happen around the village, strange for him and most of the civilians around Konohagakure. Apparently, Naruto's daily pranks have completely stopped. Not a single Naruto's traditional orange pranks have appeared in a little over a month. It's like he vanished, a thought that completely tore Hiruzen's heart.

Anyone who's ever met the boy knows how much of a prankster Naruto can be, the six-year-old boy was _known_ for his ambitious pranks around the entire village; no one was safe from him. However, he doesn't just _stop_ pranking – his favorite past time and hobby – all the sudden, Naruto doesn't work like that. This is what made Hiruzen worry about what could become. He had gotten word from ANBU's that they had had sight of Naruto with Danzō about a month and a half ago but, after that, absolutely nothing. The Third Hokage would have to wait till the meeting in a few minutes to consult Danzō about it.

He put out the smoke, pocketing the pipe in a secure location on his person. The older man headed for the conference room where all the shinobi council and most of the civilian council were found sitting, quietly talking amongst themselves. However, silence filled the room once he entered. Hiruzen gave them a small smile, "Good morning, the monthly meeting is now in session."

The civilian council representative – who came upon the spot about two and a half years ago – stood up hastily, wishing to talk about the economy and certain trivial things that did not relate to the shinobi council whatsoever. Hiruzen listened with mild interest, noting that trading with Sunagakure had increased significantly. They did mention the quick rise of Otogakure – the Village Hidden in the Sound – coming from seemingly nowhere. Other villages were trying to get Otogakure to sign an alliance with them but none have been successful. The civilian council thinks that a large, new village would be good for a new alliance after everything that had gone down with Iwagakure, Kirigakure, and Kumogakure over the last few years. Hiruzen and several of the other shinobi in the room explained that it has already been taken care of and to move on with it. However, there was nothing else that the civilian council wished to discuss anymore before going silent.

The Third Hokage turned to look at the right side of the room, shinobis looking up at him from their seats. "What do you have to present to the room?" He questioned.

Shikaku stood up, "The shinobi council would like to deliberate about the mysterious disappearance of one Naruto Uzumaki."

The old Sarutobi man narrowed his eyes, having thought of the same thing, "Go on."

"I'm sure all of us inside this room have noticed the significant lack of pranks that have affected those inside the village walls from Naruto. Most of us would feel elated that we do not have to deal with orange paint splatters and graffiti on the Hokage Mountain but that does not give us peace." The Nara stated factually, "What this _does_ give us is a worrying sense of mystery surrounding his sudden disappearance. ANBU's have stated that the last known person seen with Naruto Uzumaki is Danzō Shimura. Do you care to explain, Danzō-san?" He sat down after finishing his words.

Danzō did not stand up to speak in the room, saying that it was old bones or the likes of, "Do not worry yourselves too much as to where Naruto is; he is fine, healthy, and is happier."

"Where exactly is he?" The Third Hokage narrowed his eyes.

"In a ROOT operative base hidden somewhere in Konoha." The room fell silent immediately after the words left the older man's mouth. He looked completely serious and oddly bored as if the words he was speaking were of trivial things.

"Danzō, I'm sure you remember what we discussed when Naruto was put into the village's possession," Hiruzen stated, a growl being forced back.

He smirked, "Of course, I remember things quite well. You specifically said that he couldn't be trained under me without either your permission or his consent."

The old Sarutobi man's eyes widened significantly, abruptly standing up, "Naruto would _never_ give you permission for him to train under you. You only just met about a month and a half ago."

"What can I say, the kid trusts me." Danzō shrugged, "If you don't believe me, I have a consent form that he signed the day after he agreed to train under me for legal reasons." He reached into his pocket, pulling out a single, folded piece of paper, sliding it towards the Hokage. "It expires in five years. By then, he should be a ROOT operative and be legally considered an adult by use of ninja status; he'll be able to decide whether he'd like to stay with ROOT or do as he please." Danzō explains, "However, I'm sure he's not going to leave."

Hiruzen read over the consent form, recognizing the large and bouncy signature of Naruto, having had the boy sign a few things as he was growing up. His eyes darkened, "Danzō, did you trick Naruto into signing this in any shape or form? Threats? Promises that you can't keep?"

"Not at all, old friend." He raised an eyebrow, "Why, do you not trust the kid's judgment? He's smarter than he looks."

"I know that since I've spent a lot of time with him as he was growing up." He stated with a monotone voice.

"Then allow him to do what he wants. If he wants to join ROOT and train under me, then so be it." Danzō shrugged, "Don't fret over it, old friend."

The Third Hokage narrowed his eyes, "If I find out that he did not join of his own free will, so help me, you will not live to see the next light of day. Do you understand me?"

"Absolutely."

He sighed, sitting down, "The mysterious disappearance of Naruto Uzumaki has been solved, continue with the meeting."

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 **If you have any questions, comment them and I will answer them in the next chapter.**


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